Repositories list

• LFF_spatial_ERC

  Public
  LFF_spatial_ERC

  HTML

  •

  MIT License

  •0•1•0•0•Updated Feb 19, 2026Feb 19, 2026

• LFF_spatial_LC

  Public
  LFF project, spatial_LC data analysis

  HTML

  •0•0•0•0•Updated Feb 18, 2026Feb 18, 2026

• spatialdACC

  Public
  spatialdACC project

  HTML

  •0•0•0•0•Updated Feb 18, 2026Feb 18, 2026

• spatialDLPFC_SCZ

  Public
  Visium-IF/RNAscope-IF project looking at spatial gene expression in the context of perineuronal nets in DLPFC of neurotypical control donors and donors with a d…

  HTML

  •0•0•16•0•Updated Feb 16, 2026Feb 16, 2026

• spatial_HYP

  Public
  HTML

  •0•1•0•0•Updated Feb 16, 2026Feb 16, 2026

• globus

  Public
  LIBD Globus Share Endpoints

  HTML

  •1•0•0•0•Updated Feb 13, 2026Feb 13, 2026

• Posit_Connect_shiny_apps

  Public
  Code for Posit Connect R shiny apps (spatialLIBD, iSEE, ...)

  R

  •0•0•0•0•Updated Feb 3, 2026Feb 3, 2026

• Habenula_Pilot

  Public
  habenulaPilot project code repository

  rna-seqschizophreniabulk-rna-seq+ 2snrna-seqhabenula

  HTML

  •1•0•0•0•Updated Jan 27, 2026Jan 27, 2026

• spatial_NAc

  Public
  Paired snRNA-seq/Visium for human NAc

  HTML

  •0•0•1•0•Updated Jan 26, 2026Jan 26, 2026

• jhpce_module_config

  Public
  JHPCE module configuration files

  Lua

  •0•4•0•0•Updated Jan 21, 2026Jan 21, 2026

• jhpce_module_source

  Public
  JHPCE module source files

  Shell

  •0•0•0•0•Updated Jan 21, 2026Jan 21, 2026

• spatialLIBD

  Public
  Code for the spatialLIBD R/Bioconductor package and shiny app

  shinyrstatsbioconductor+ 6golem10xgenomicsspatial-transcriptomicsvisiumspatiallibdspatialexperiment

  R

  •22•109•25•1•Updated Jan 15, 2026Jan 15, 2026

• Brain_INTERACT

  Public
  Python

  •0•0•0•0•Updated Jan 14, 2026Jan 14, 2026

• bdportal

  Public
  Brain data portal at LIBD. Not only brain data.

  JavaScript

  •0•0•2•0•Updated Jan 12, 2026Jan 12, 2026

• tsc-cellpainting

  Public
  iTSC cell painting project

  R

  •0•0•0•0•Updated Jan 9, 2026Jan 9, 2026

• fentanyl_rat_hb_amy

  Public
  Roff

  •0•0•0•0•Updated Dec 11, 2025Dec 11, 2025

• SPEAQeasy

  Public
  SPEAQeasy: portable LIBD RNA-seq pipeline using Nextflow. Check http://research.libd.org/SPEAQeasy-example/ for an example on how to use this pipeline and analy…

  pipelinenextflowrstats+ 4rnaseqhisat2rna-seq-pipelinespeaqeasy

  HTML

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  MIT License

  •5•6•21•0•Updated Dec 10, 2025Dec 10, 2025

• BiocMAP

  Public
  Our typical analysis steps for WGBS data, starting from FASTQ reads and ending with the construction of bsseq objects. Created using nextflow

  nextflowwgbs

  HTML

  •1•3•4•0•Updated Dec 10, 2025Dec 10, 2025

• dRFEtools

  Public
  dynamic Recursive Feature Elimination tools

  Python

  •

  GNU General Public License v3.0

  •2•1•0•0•Updated Nov 30, 2025Nov 30, 2025

• spatialDLPFC

  Public
  spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples

  rstatsbioconductortranscriptomics+ 5spatial-transcriptomicsvisiumdlpfcspatialdlpfcvisium-spg

  HTML

  •5•29•1•0•Updated Nov 21, 2025Nov 21, 2025

• spatial_hpc

  Public
  Repository for the spatial (U01) hippocampus (hipc) project

  HTML

  •3•8•1•0•Updated Oct 31, 2025Oct 31, 2025

• visiumStitched

  Public
  R package containing functions useful for stitching Visium capture areas. Related to the example human brain data described at http://research.libd.org/visiumSt…

  rstatsbioconductor10xgenomics+ 4spatial-transcriptomicsvisiumspatiallibdspatialexperiment

  R

  •0•4•2•0•Updated Oct 13, 2025Oct 13, 2025

• qsvaR

  Public
  Quality Surrogate Variable Analysis for Degradation Correction

  humanrstatsbioconductor+ 3braindegradationqsva

  R

  •2•0•15•0•Updated Sep 30, 2025Sep 30, 2025

• recount3

  Public
  Explore and download data from the recount3 project

  countgener+ 12humanmouserstatsbioconductorrnaseqilluminaexon+ 5

  R

  •5•37•20•0•Updated Sep 24, 2025Sep 24, 2025

• visiumStitched_brain

  Public
  Example human brain data used for https://research.libd.org/visiumStitched/.

  spatialrstatsbioconductor+ 4transcriptomicsvisiumspatiallibdvisiumstitched

  HTML

  •0•1•0•0•Updated Sep 23, 2025Sep 23, 2025

• recount3-docs

  Public
  Documentation for all things related to `recount3`

  humanmouserstats+ 7bioconductorrnaseqrecounthg38recount2mm10recount3

  R

  •2•3•0•0•Updated Sep 22, 2025Sep 22, 2025

• BLA_crossSpecies

  Public
  Collaboration between Costa, Martinowich, and Hicks labs investigating basolateral amygdala cell-types across huamn and non-human primate species.

  R

  •0•5•0•0•Updated Sep 18, 2025Sep 18, 2025

• Brain_WGCNA

  Public
  Scripts for the WGCNA paper: Schizophrenia risk genes converge into divergent co-expression pathways reflecting brain development across regions and age period…

  R

  •0•5•0•0•Updated Sep 10, 2025Sep 10, 2025

• smoking-nicotine-mouse

  Public
  Smoking mouse project

  R

  •0•1•1•0•Updated Sep 9, 2025Sep 9, 2025

• smokingMouse

  Public
  Provides access to smokingMouse project raw and processed data objects

  R

  •0•1•0•0•Updated Sep 8, 2025Sep 8, 2025